The kitchen/baking section of the Shibuya Tokyu Hands is called "3C" which is sort of the 3rd floor - you'll see when you get there, and they have all kinds of crumpet rings, egg rings, cake tins, even powdered egg whites, edible glitter and pre-made frozen sponge cake. You can get an instant read thermometer here too, somewhat away from the baking area near the peelers and storage jars. Ah! Also, in my failed attempts to find cake tins in Tokyo, I discovered that Tokyu Hands is also the best place for over-sized tupperware.

My digital thermometer (in its holder)

Loft
A trendier shop than Tokyu Hands, great for novely gifts, Loft also has a good baking section with many varieties of cake pans and measuring equipment, some of which are imported. I usually visit the Shibuya Loft, but noticed that one opened up replacing Laox next to Muji in Yurakucho.

The cake tin and tray section of Loft, Shibuya

Nissin
More useful to you as a supplier of your strong bread flour, molasses, vegetable shortening and imported cake mixes, Nissin also has a small household goods section on the ground floor next door to the main shop. The baking section is right at the back and they have a few, mainly ring-cake type, cake tins (with holes in the middle). They do have some cupcake cases that don't require muffin tins to rest in, and they also have some disposable foil and paper trays for baking in. Many of the baking sheets at Nissin are American oven-sized, so make sure that you've measured the inside of your oven before buying! Nissin also sell some nice gift boxes, including some cupcake boxes (single and x4 cake variations), which are currently stored near the greetings cards.

Nissin's baking section. Check out that pastry board!

Marusei
In the Musashi Koyama "Palm" shopping centre (what a name), there is a fantastic shop called Marusei with aisles of cooking equipment, from the sharp knife aisle, the many-varieties of frying pan aisle to the glass bowl and jugs area. Prices are reasonable and it's definitely worth a look if you're in the area. Don't forget to drop by the bakery Nemo, not far from Musashi Koyama station, for some excellent bread.

100-yen shops
The trusty hundred yen shop is worth checking for their disposable paper cake cases, small bowls, peelers and zesters. You can get a decent pestle and mortar (100 yen each for the mortar and the pestle, not complaining..), and depending on the shop in question they may also have smaller cake tins, various utensils, and rammekins, possibly heart-shaped. The biggest 100 yen shop I know of is the Daiso shop near Harajuku station (map). You can get *everything* there.

A 100 Yen shop in Azabu Juban

Failing the above, and in some cases preferable to them, it's also worth working out whether it makes sense to have items shipped to you from overseas. I recently saved about half the price I would have paid in Tokyo for a La Creuset casserole that was on sale in my current favourite UK based baking supply shop, Lakeland. That included overseas delivery to my door! Lakeland have excellent quality bake ware, professional piping bags, cake stands, mixers, classy ceramic shortbread molds... Just be sure to measure the inside of your oven when ordering any baking trays!